E484, F490, Q493, and S494 are the 4 amino acid residues within the Spike receptor-binding motif (RBM) that are known to be critical for bamlanivimab binding. Q493 is also among the many more RBM residues crucial for interactions with etesivimab. Q493R/K (which can be selected in vitro by bamlanivimab3, C121, or C1444) is to date the only mutation that causes resistance to both bamlanivimab and etesivimab. It also causes resistance to other class 3 monoclonal antibodies5, i.e. the ones that do not overlap with ACE2 binding site and have accessibility to RBD epitope in “up”/”down” conformations. More in detail, in pseudoviral neutralization assays Q493R reduces susceptibility to bamlanivimab by > 6,666 folds, to etesevimab by 232 folds, and to the combination of both by > 100 folds2; accordingly, in a flow cytometry competitive assay, Q493R reduces IC50 of > 100 folds for bamlanivimab and 42 folds for etesivimab3.
Q493R has a frequency of 0.006% in the GISAID database (85 out of 1,424,998 deposited sequences as of May 8, 2021; https://covid19dashboard.regeneron.com/?tab=Mutation_Details&subTab=Spike), making the occurrence of co-infection from a Q493R-positive strain extremely unlikely in our patient.
In conclusion, we have shown here that mutations conferring resistance to both bamlanivimab and etesevimab can arise in vivo: Q493 mutations increase binding affinity to ACE2 6, but further studies are needed to clarify whether such escape mutants are fit enough to spread and persist in humans. Genomic surveillance for SARS-CoV-2 variants is encouraged in COVID-19 patients showing refractoriness to anti-Spike monoclonal antibodies.